Short- and long-read metagenomics expand individualized structural variations in gut microbiomes

作者：Liang Chen, Na Zhao, Jiabao Cao, Xiaolin Liu, Jiayue Xu, Yue Ma, Ying Yu, Xuan Zhang, Wenhui Zhang, Xiangyu Guan, Xiaotong Yu, Zhipeng Liu, Yanqun Fan, Yang Wang, Fan Liang, Depeng Wang, Linhua Zhao, Moshi Song, Jun Wang · 发表于：Nature Communications · 年份：2022 · DOI：10.1038/s41467-022-30857-9 · 被引用次数：122 · 研究领域：Gut microbiota and health、Microbial Community Ecology and Physiology、Genomics and Phylogenetic Studies

In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome.